Dear Sir or Madam:
The MCSE is becoming increasingly passe as it applies only to Windows Server 2003 and earlier versions. For Windows Server 2008 (the current version since it shipped last February) the newer MS certifications are called the MCTS, or Microsoft Certified Technology Specialist, and MCITP, or ...Information Technology Professional). I wouldn't recommend spending good money on the MCSE any longer. That said, the CCNA is just an entry-level Cisco cert and by itself probably won't be enough to do you a lot of good in landing a network engineer job (It's more or less irrelevant to software engineering topics, except in the most basic ways).
If you're interested in programming, then the newer Microsoft programming certifications (see the discussion online at http://www.microsoft.com/learning/mcp/default.mspx#CERT where you'll find coverage of both networking and software engineering credentials included) may indeed make significant sense. Here again, however, I'd urge you to look at the technology specialist and Professional Developer certifications that you'll find covered on the aforementioned Web page.
As for which pays better, it depends on how far you advance in the field and what kind of work you are most interested in doing. I don't think it's really possible to say that if you choose one path over the other you will make more or less money, simply because there are so many options on both the networking and development sides, and you can early well into the 100,000s going either way.
HTH, and thanks for posting. Please post again if you have any follow-up comments, questions, or concerns.